Sat Oct 15 12:34:48 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 15 2011 at 12:34:48 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2220 !!! WARNING: NAP 207 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7027518 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -16.72100 31.15300 ymin,ymax (A): -20.21300 30.44500 zmin,zma (A): -4.573000 34.94600 x,y,z range (A): 47.87400 50.65800 39.51900 scale (grids/A): 0.7027518 object centre (A): 7.216000 5.116000 15.18650 number of atom coordinates read : 2220 total number of charged atoms : 2083 net assigned charge : 6.000018 assigned positive charge : 334.1085 centred at (gu) : 89.90016 90.75582 90.84238 assigned negative charge : -328.1089 centred at (gu) : 89.80647 90.85201 90.96528 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7350 nv = 96 ne = 84 npr = 45987 no. pairs analyzed = 45987 no. exposed pairs = 2660 no. arc points = 19136 no. surface atoms = 904 nbur = 1316 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 502 mr = 4102 m= 7 mr = 100 m= 0 mr = 0 time to grow re-entrant surface = 8.9999996E-02 no. cavity mid-points inaccessible to solvent = 193 time to turn everything in is 0.1900000 number of dielectric boundary points 3657 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1817 ## 161 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8341 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.7454495E-08 -1.4616974E-08 midg,1,midg; midg,igrid,midg 7.8433672E-08 5.5960786E-10 1,midg,midg; igrid,midg,midg 2.0724940E-09 8.7949331E-08 gauss-seidel spectral radius is 0.9894643 estimated iterations to convergence 79 setup time was (sec) 0.3900000 now iterating at: 12:34:49 rms-change max change #iterations 0.2039605 31.37300 at 10iterations 2.4676608E-02 3.150357 at 20iterations 2.9624994E-03 0.3727102 at 30iterations 3.6162141E-04 5.0983429E-02 at 40iterations 4.3970162E-05 5.6915283E-03 at 50iterations finished qdiffx linear iterations at : 12:34:54 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 4.3970162E-05 5.6915283E-03 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.490000 DelPhi exited at 12:34:55 3.493u 0.194s 0:06.81 54.0% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 15 2011 at 12:34:55 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2220 !!! WARNING: NAP 207 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.108255 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -16.72100 31.15300 ymin,ymax (A): -20.21300 30.44500 zmin,zma (A): -4.573000 34.94600 x,y,z range (A): 47.87400 50.65800 39.51900 scale (grids/A): 2.108255 object centre (A): 7.216000 5.116000 15.18650 number of atom coordinates read : 2220 total number of charged atoms : 2083 net assigned charge : 6.000018 assigned positive charge : 334.1085 centred at (gu) : 89.70041 92.26694 92.52682 assigned negative charge : -328.1089 centred at (gu) : 89.41936 92.55611 92.89589 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 78156 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19136 grid for indexing accessible points = 1.400000 m= 30356 mr = 54192 m= 6202 mr = 23021 m= 613 mr = 4292 m= 26 mr = 302 m= 0 mr = 3 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 4144 time to turn everything in is 0.4200000 number of dielectric boundary points 33543 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 93 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 16575 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.7027518 object centre at (A) : 7.216000 5.116000 15.18650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.1241057E-02 2.5381124E-02 midg,1,midg; midg,igrid,midg 3.6460947E-02 1.0120967E-02 1,midg,midg; igrid,midg,midg -1.0029244E-02 3.5017375E-02 gauss-seidel spectral radius is 0.9988346 estimated iterations to convergence 232 setup time was (sec) 0.6800000 now iterating at: 12:34:56 rms-change max change #iterations 4.779971 238.2279 at 10iterations 2.353611 91.11871 at 20iterations 1.167440 34.12661 at 30iterations 0.5796660 17.71711 at 40iterations 0.2874389 8.611439 at 50iterations 0.1428925 4.509488 at 60iterations 7.0975333E-02 2.033142 at 70iterations 3.5003010E-02 1.117624 at 80iterations 1.7372036E-02 0.4910617 at 90iterations 8.5931085E-03 0.2430954 at 100iterations 4.2720418E-03 0.1261377 at 110iterations 2.1210632E-03 6.3278198E-02 at 120iterations finished qdiffx linear iterations at : 12:35:04 total time elapsed so far: 8.840000 # loops : 120 mean,max change (kT/e) : 2.1210632E-03 6.3278198E-02 energy calculations done at 8.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.970000 DelPhi exited at 12:35:05 8.975u 0.276s 0:09.57 96.5% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 15 2011 at 12:35:05 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2220 !!! WARNING: NAP 207 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.162383 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -16.72100 31.15300 ymin,ymax (A): -20.21300 30.44500 zmin,zma (A): -4.573000 34.94600 x,y,z range (A): 47.87400 50.65800 39.51900 scale (grids/A): 3.162383 object centre (A): 7.216000 5.116000 15.18650 number of atom coordinates read : 2220 total number of charged atoms : 2083 net assigned charge : 6.000018 assigned positive charge : 334.1085 centred at (gu) : 89.55042 93.40018 93.79033 assigned negative charge : -328.1089 centred at (gu) : 89.12903 93.83413 94.34383 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 180128 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19136 grid for indexing accessible points = 1.400000 m= 94471 mr = 130476 m= 38723 mr = 78508 m= 11937 mr = 31952 m= 2456 mr = 9429 m= 313 mr = 1831 m= 20 mr = 192 m= 0 mr = 8 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 14598 time to turn everything in is 1.290000 number of dielectric boundary points 75652 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.410000 number of grid points assigned charge 16664 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 2.108255 object centre at (A) : 7.216000 5.116000 15.18650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5646782 0.2521409 midg,1,midg; midg,igrid,midg 0.3057184 0.2447626 1,midg,midg; igrid,midg,midg -2.4492485E-02 0.2442089 gauss-seidel spectral radius is 0.9992895 estimated iterations to convergence 296 setup time was (sec) 1.580000 now iterating at: 12:35:07 rms-change max change #iterations 10.38855 464.8469 at 10iterations 6.029523 124.0640 at 20iterations 3.492357 65.76133 at 30iterations 2.026801 34.31993 at 40iterations 1.177832 19.72477 at 50iterations 0.6812496 11.58328 at 60iterations 0.3954316 7.460692 at 70iterations 0.2296004 4.008993 at 80iterations 0.1328823 2.245546 at 90iterations 7.7316113E-02 1.361167 at 100iterations 4.4708639E-02 0.7966909 at 110iterations 2.5978049E-02 0.4144861 at 120iterations 1.5071993E-02 0.2671299 at 130iterations 8.7585747E-03 0.1461029 at 140iterations 5.0705248E-03 9.8773956E-02 at 150iterations 2.9380422E-03 4.9118042E-02 at 160iterations 1.7074798E-03 2.9951096E-02 at 170iterations 9.8968972E-04 1.6555786E-02 at 180iterations finished qdiffx linear iterations at : 12:35:20 total time elapsed so far: 15.00000 # loops : 180 mean,max change (kT/e) : 9.8968972E-04 1.6555786E-02 energy calculations done at 15.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.13000 DelPhi exited at 12:35:20 15.127u 0.280s 0:15.70 98.0% 0+0k 0+0io 0pf+0w